When Santa Clara County's longtime chief pediatrician for abused and neglected children was dismissed two years ago, officials offered little explanation -- just an ominous letter from the district attorney warning there was "substantial evidence" that he "committed multiple crimes involving moral turpitude, specifically sexual assaults."

Now, for the first time, lurid details of child molestation allegations against Dr. Patrick Clyne have emerged in court documents, and one of several foster children who lived with Clyne has come forward to describe to this newspaper abuse that he says has "taken my whole life" to overcome.

The new details deepen the mystery surrounding Clyne, 52, who had many defenders at the time of his dismissal, was never charged with a crime, and now works in private practice just 50 miles away in Watsonville. Serious questions are emerging about how authorities handled his case -- and whether they have done enough, now and in the past, to protect the children he treats.

"I can't believe the justice system is like this, that they let this go on," said Kyle, who lived with Clyne from fourth through ninth grade. Now 27, Kyle said he testified before a grand jury in 2002 that Clyne molested him. The newspaper is using only Kyle's first name to protect his privacy. "If I could prevent him from hurting one more kid," Kyle said, "that's my mission accomplished."

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The most extensive accounts of Clyne's alleged misdeeds have shown up in an unexpected place -- a habeas corpus petition filed in the 6th District Court of Appeal that challenges Clyne's credibility as a key witness in helping convict child-killer Emmanuel Brew in 2008.

According to that filing, which is based on confidential law enforcement reports of two separate investigations of Clyne, three of the four foster boys placed in Clyne's care told police he had abused them.

Years later, six patients, ages 5 through 10, reported the pediatrician "had shown inappropriately enthusiastic interest in their privates when he examined them and no one else was present," according to records cited in the court petition.

Clyne denies the accusations. Reached at his Watsonville office, he described the allegations as "fantasy" and "fiction" depicting "someone I'm completely unfamiliar with."

"I can say unequivocally I have never touched any child inappropriately in the office or ever," Clyne said. If the allegations were true, he added, "I would have been arrested. And I wasn't."

But scrutiny may now grow for the wheelchair-bound physician who cared for thousands of Santa Clara County foster children, and took boys into his home as a single foster father.

One of the biggest questions about his case persists: Why did the district attorney, despite clear suspicions that Clyne had molested children, never prosecute him?

Assistant District Attorney David Angel said it came down to proving the case: "The reason he was never charged is that while we believe there is substantial evidence that he committed the crime, we do not believe that there is sufficient evidence to prove his guilt beyond a reasonable doubt." A grand jury heard the first round of allegations in 2002 but failed to return an indictment of Clyne because it "did not believe there was enough evidence."

However, in 2011, the DA's office announced that an internal committee of prosecutors had placed Clyne on a list of its potentially impeachable witnesses and, by law, informed defense attorneys why they believe he had a tainted past. Previously the office had used Clyne as an expert witness in at least 12 child abuse cases.

The November habeas petition by Brew's attorney, David Martin, reveals for the first time some of the evidence behind the DA's concerns about Clyne. In addition to the interviews with Clyne's own foster children, it shows that in 2009, four children, ages 8 to 10, described inappropriate genital exams. Two similar reports surfaced in 2010, including one from a boy who was 5 at the time. The court records describe girls' statements that they were required to squat in a "frog" position while the doctor touched their genitals.

Clyne said in an interview that examining girls this way is acceptable practice; he suggested that investigators might have asked "leading" questions. Clyne added that he is now more diligent about always having another adult in the room during sensitive exams and documenting that. But another physician consulted by investigators described his exams as "ridiculous," "insensitive" and "bizarre," court documents show.

By all accounts, Clyne is no ordinary physician. Plenty praise the affable doctor who was disabled in a rock-climbing accident as a medical resident. During his 14-year tenure inï»¿ Santa Clara County, Clyne earned trust among foster parents who appreciated his expertise and 24/7 availability.

Longtime foster mother Dawn Haddaway, who reviewed the new court documents, called the allegations "unsubstantiated."

"I have complete confidence in him as a person, as well as a pediatrician," Haddaway said. "The county lost one of its best."

Yet, County Executive Jeff Smith said the newly revealed descriptions of abuse are "extremely disturbing," and he now has "considerable concerns" Clyne is still practicing.

Medical Board of California spokeswoman Cassandra Hockenson would not discuss whether Clyne's license was under review, citing privacy laws. The board can suspend a physician's license after an arrest through the criminal courts or if it believes there is an immediate threat to patient safety. Doctors have a right to an administrative hearing before their licenses can be revoked.

The earliest and most extensive allegations against Clyne focus not on patients, but on the young boys he lived with.

Those allegations first surfaced in 2001. In Kyle's case, his juvenile probation officer reported the boy's complaints after he had reunited with his mother out of state. According to the court reports, when Kyle first recounted being fondled in bed by Clyne, he burst into tears and vomited. Later interviewed by police, the teen cried and told his mother that "he was sorry for letting (Dr. Clyne) touch him."

The sexual abuse began around age 9, Kyle said, after he got scared one night and went to Clyne's room for comfort. After falling asleep, he told a reporter, "I woke up and felt him touching me -- and I thought it was a nightmare."

A second boy placed briefly with Clyne by the child welfare agency "reported seven to eight incidents where Dr. Clyne would try to touch his genital area," the records state. The court reports describe the boy's account that "Dr. Clyne would roll his wheelchair toward him and act as if his hand accidentally slipped off, successfully touching his crotch on two occasions."

One of the four boys who lived with Clyne denied there had been abuse. At one point in the investigation when police arrived at Clyne's home, the boy had apparently been drinking Scotch, and was "wearing a lot of silver jewelry that Dr. Clyne had bought him," the records show. He told police Clyne was "the only one who had ever given him anything."

A fourth boy, who moved in with Clyne at age 9 and eventually ran away, also initially denied any abuse. But when investigators interviewed him in person days later he acknowledged that on multiple occasions "he would wake up at night to discover Clyne touching his penis,'' the brief states. In one exchange quoted in the court files, the boy reacted angrily, and knocked Clyne's hand away; Clyne then responded, "Oh it fell out I was just putting it away."

The boy's mother, Tonya Batorski, said she learned of the abuse allegations when her son testified before the grand jury. Before that, she said she was grateful to Clyne, who took her son in when she suffered from alcohol abuse and couldn't care for him.

But after a few years, Batorski said, "everything just went haywire." The boy became increasingly defiant, failing school. He was killed at 18 in a gang-related shooting. "I feel so bad for my son and for all those kids," Batorski said.

Kyle's relatives said he too changed dramatically. "He was a well-adjusted, happy, joyful young boy" when he went to Clyne's, his grandfather Paul Fisher ï»¿said. A year later, "All of a sudden that boyhood joy and charm was gone."

Kyle, now living in the Bay Area, said the abuse has resulted in years of therapy for depression, post-traumatic stress and pent-up rage that's led to trouble with the law. But as a boy, he said, "I didn't know it was wrong -- I was too young to even know what was going on. It's taken my whole life until this point to overcome it."

Contact Karen de Sá at 408-920-5781.

DOCTOR's ROCKY TENURE

1996: Dr. Patrick Clyne begins working for county-run Santa Clara Valley Medical Center. 2001: Clyne is suspended while San Jose police investigate reports of sexual abuse by three boys placed by child welfare agency in Clyne's home.2002: A Santa Clara County grand jury hears two days of testimony but does not indict Clyne.2009-2010: A second set of sexual abuse allegations emerges, this time from six of Clyne's child patients.2010: Clyne is suspended for a second time while police investigate the claims.2011: Santa Clara County district attorney notifies county it has "substantial evidence that Dr. Clyne committed multiple crimes involving moral turpitude, specifically sexual assaults." County dismisses Clyne, and a county hospital official alerts the California Medical Board. 2013: Clyne opens Pediatric Medical Group of Watsonville with another physician. One month later, first extensive details of abuse allegations against Clyne appear in habeas corpus petition from child killer appealing a murder conviction.